Tight-binding molecular-dynamics studies of defects and disorder in covalently-bonded materials

Tight-binding (TB) molecular dynamics (MD) has emerged as a powerful method for investigating the atomic-scale structure of materials --- in particular the interplay between structural and electronic properties --- bridging the gap between empirical methods which, while fast and efficient, lack transferability, and ab initio approaches which, because of excessive computational workload, suffer from limitations in size and run times. In this short review article, we examine several recent applications of TBMD in the area of defects in covalently-bonded semiconductors and the amorphous phases of these materials.Comment: Invited review article for Comput. Mater. Sci. (38 pages incl. 18 fig.

Identification of relaxation and diffusion mechanisms in amorphous silicon

The dynamics of amorphous silicon at low temperatures can be characterized by a sequence of discrete activated events, through which the topological network is locally reorganized. Using the activation-relaxation technique, we create more than 8000 events, providing an extensive database of relaxation and diffusion mechanisms. The generic properties of these events - size, number of atoms involved, activation energy, etc. - are discussed and found to be compatible with experimental data. We introduce a complete and unique classification of defects based on their topological properties and apply it to study of events involving only four-fold coordinated atoms. For these events, we identify and present in detail three dominant mechanisms.Comment: 4 pages, three figures, submitted to PR

Amorphous silicon under mechanical shear deformations: shear velocity and temperature effects

Mechanical shear deformations lead, in some cases, to effects similar to those resulting from ion irradiation. Here we characterize the effects of shear velocity and temperature on amorphous silicon (\aSi) modelled using classical molecular dynamics simulations based on the empirical Environment Dependent Inter-atomic Potential (EDIP). With increasing shear velocity at low temperature, we find a systematic increase in the internal strain leading to the rapid appearance of structural defects (5-fold coordinated atoms). The impacts of externally applied strain can be almost fully compensated by increasing the temperature, allowing the system to respond more rapidly to the deformation. In particular, we find opposite power-law relations between the temperature and the shear velocity and the deformation energy. The spatial distribution of defects is also found to strongly depend on temperature and strain velocity. For low temperature or high shear velocity, defects are concentrated in a few atomic layers near the center of the cell while, with increasing temperature or decreasing shear velocity, they spread slowly throughout the full simulation cell. This complex behavior can be related to the structure of the energy landscape and the existence of a continuous energy-barrier distribution.Comment: 10 pages, 17 figure

Mitigating Alzheimer’s disease with natural polyphenols: a review

According to Alzheimer’s Disease International (ADI), nearly 50 million people worldwide were living with dementia in 2017, and this number is expected to triple by 2050. Despite years of research in this field, the root cause and mechanisms responsible for Alzheimer’s disease (AD) have not been fully elucidated yet. Moreover, promising preclinical results have repeatedly failed to translate into patient treatments. Until now, none of the molecules targeting AD has successfully passed the Phase III trial. Although natural molecules have been extensively studied, they normally require high concentrations to be effective; alternately, they are too large to cross the blood-brain barrier (BBB). In this review, we report on AD treatment strategies, with a virtually exclusive focus on green chemistry (natural phenolic molecules). These include therapeutic strategies for decreasing amyloid- β (Aβ) production, preventing and/or altering A β aggregation, and reducing oligomers cytotoxicity such as curcumin, (-)- epigallocatechin-3-gallate (EGCG), morin, resveratrol, tannic acid, and other natural green molecules. We also examinewhether consideration should be given to potential candidates used outside of medicine and nutrition, through a discussion of two intermediate-sized green molecules, with very similar molecular structures and key properties, which exhibit potential in mitigating Alzheimer’s disease

Thermally-activated charge reversibility of gallium vacancies in GaAs

The dominant charge state for the Ga vacancy in GaAs has been the subject of a long debate, with experiments proposing $-$1, $-$2 or $-$3 as the best answer. We revisit this problem using {\it ab initio} calculations to compute the effects of temperature on the Gibbs free energy of formation, and we find that the thermal dependence of the Fermi level and of the ionization levels lead to a reversal of the preferred charge state as the temperature increases. Calculating the concentrations of gallium vacancies based on these results, we reproduce two conflicting experimental measurements, showing that these can be understood from a single set of coherent LDA results when thermal effects are included.Comment: 4 pages, 4 figure

Understanding long-time vacancy aggregation in iron: a kinetic activation-relaxation technique study

Vacancy diffusion and clustering processes in body-centered-cubic (bcc) Fe are studied using the kinetic activation-relaxation technique (k-ART), an off-lattice kinetic Monte Carlo method with on-the-fly catalog building capabilities. For monovacancies and divacancies, k-ART recovers previously published results while clustering in a 50-vacancy simulation box agrees with experimental estimates. Applying k-ART to the study of clustering pathways for systems containing from one to six vacancies, we find a rich set of diffusion mechanisms. In particular, we show that the path followed to reach a hexavacancy cluster influences greatly the associated mean-square displacement. Aggregation in a 50-vacancy box also shows a notable dispersion in relaxation time associated with effective barriers varying from 0.84 to 1.1 eV depending on the exact pathway selected. We isolate the effects of long-range elastic interactions between defects by comparing to simulations where those effects are deliberately suppressed. This allows us to demonstrate that in bcc Fe, suppressing long-range interactions mainly influences kinetics in the first 0.3 ms, slowing down quick energy release cascades seen more frequently in full simulations, whereas long-term behavior and final state are not significantly affected.Comment: 11 pages, 12 figures. Updated to post-review manuscrip